Ailanthus altissima var. erythrocarpa is one of Ailanthus altissima varieties with high economic, ecological and ornamental value. In this study, transcriptome analysis was used to develop SSR primers. Based on this, 34 Samara species with different redness were selected as research objects to screen polymorphic SSR primers and construct their fingerprints. Transcriptomic analysis revealed 10681 SSR loci, of which mononucleotide repeats were dominant (58.3%), followed by dinucleotide and

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... eotide repeats (16.6%, 15.1%), and pentanucleotide repeats were the lowest (0.2%). The PCR amplification system of est-ssr primers was (total volume 20μl), DNA 3μl (30ng/μl), 2 ×Taq PCR Master Mix 10μl, upstream and downstream primers each 1μl (10μmol/μl), ddH2O 5μl. Among 140 pairs of primers randomly selected, 13 pairs of core primers with good polymorphism were selected. The average number of alleles (Na), the average number of effective alleles (Ne), the average Shannon's diversity index (I), the average observed heterozygosity (Ho), the average expected heterozygosity (He), the fixed index (F) and the polymorphic information content (PIC) were as follows: 4.462, 3.067, 1.227, 0.402, 0.659, 0.391, 0.603. Among 13 pairs of primers, 4 pairs (P33, P69, P79, p95) could effectively distinguish and construct the fingerprint of the tested materials. This study is of great significance for the genetic structure, genetic diversity analysis, evolutionary history, germplasm conservation and germplasm innovation of Ailanthus altissima var. erythrocarpa.